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論文リスト

doi title author source_title year
4215 10.1016/j.cell.2018.05.061 Recovering Gene Interactions From Single-Cell Data Using Data Diffusion Cell 2018
4220 10.1016/j.cell.2018.06.052 A Single-Cell Atlas Of In Vivo Mammalian Chromatin Accessibility Cusanovich, Darren A.; Hill, Andrew J.; Aghamirzaie, Delasa; Daza, Riza M.; Pliner, Hannah A.; Berletch, Joel B.; Filippova, Galina N.; Huang, Xingfan; Christiansen, Lena; Dewitt, William S.; Lee, Choli; Regalado, Samuel G.; Read, David F.; Steemers, Frank J.; Disteche, Christine M.; Trapnell, Cole; Shendure, Jay Cell 2018
4276 10.1016/j.cell.2019.03.014 Profiling Of Pluripotency Factors In Single Cells And Early Embryos Hainer, Sarah J.; Bo<U+0161>kovi<U+0107>, Ana; Mccannell, Kurtis N.; Rando, Oliver J.; Fazzio, Thomas G. Cell 2019
4287 10.1016/j.cell.2019.05.006 Single-Cell Multi-Omic Integration Compares And Contrasts Features Of Brain Cell Identity Welch, Joshua D.; Kozareva, Velina; Ferreira, Ashley; Vanderburg, Charles; Martin, Carly; Macosko, Evan Z. Cell 2019
4290 10.1016/j.cell.2019.05.031 Comprehensive Integration Of Single-Cell Data Stuart, Tim; Butler, Andrew; Hoffman, Paul; Hafemeister, Christoph; Papalexi, Efthymia; Mauck, William M.; Hao, Yuhan; Stoeckius, Marlon; Smibert, Peter; Satija, Rahul Cell 2019
4414 10.1016/j.cell.2020.09.056 Chromatin Potential Identified By Shared Single-Cell Profiling Of Rna And Chromatin Ma, Sai; Zhang, Bing; Lafave, Lindsay M.; Earl, Andrew S.; Chiang, Zachary; Hu, Yan; Ding, Jiarui; Brack, Alison; Kartha, Vinay K.; Tay, Tristan; Law, Travis; Lareau, Caleb; Hsu, Ya-Chieh; Regev, Aviv; Buenrostro, Jason D. Cell 2020
8195 10.1016/j.molcel.2018.06.044 Cicero Predicts Cis-Regulatory Dna Interactions From Single-Cell Chromatin Accessibility Data Pliner, Hannah A.; Packer, Jonathan S.; Mcfaline-Figueroa, Jose L.; Cusanovich, Darren A.; Daza, Riza M.; Aghamirzaie, Delasa; Srivatsan, Sanjay; Qiu, Xiaojie; Jackson, Dana; Minkina, Anna; Adey, Andrew C.; Steemers, Frank J.; Shendure, Jay; Trapnell, Cole Molecular Cell 2018
8236 10.1016/j.molcel.2019.07.015 Cobatch For High-Throughput Single-Cell Epigenomic Profiling Wang, Qianhao; Xiong, Haiqing; Ai, Shanshan; Yu, Xianhong; Liu, Yaxi; Zhang, Jiejie; He, Aibin Molecular Cell 2019
12753 10.1038/s41467-018-03405-7 An Accurate And Robust Imputation Method Scimpute For Single-Cell Rna-Seq Data Li, Wei Vivian, 0000-0002-2087-2709; Li, Jingyi Jessica, 0000-0002-9288-5648 Nature Communications 2018
12887 10.1038/s41467-018-07931-2 Single-Cell Rna-Seq Denoising Using A Deep Count Autoencoder Eraslan, Gokcen, 0000-0001-9579-2909; Simon, Lukas M., 0000-0001-6148-8861; Mircea, Maria, 0000-0002-1935-8665; Mueller, Nikola S.; Theis, Fabian J., 0000-0002-2419-1943 Nature Communications 2019
12909 10.1038/s41467-018-08205-7 Deconvolution Of Single-Cell Multi-Omics Layers Reveals Regulatory Heterogeneity Liu, Longqi; Liu, Chuanyu; Quintero, Andres, 0000-0002-3959-805X; Wu, Liang; Yuan, Yue; Wang, Mingyue; Cheng, Mengnan; Leng, Lizhi; Xu, Liqin; Dong, Guoyi; Li, Rui; Liu, Yang; Wei, Xiaoyu; Xu, Jiangshan; Chen, Xiaowei; Lu, Haorong; Chen, Dongsheng; Wang, Quanlei; Zhou, Qing; Lin, Xinxin; Li, Guibo, 0000-0002-6141-4931; Liu, Shiping, 0000-0003-0019-619X; Wang, Qi; Wang, Hongru; Fink, J. Lynn; Gao, Zhengliang; Liu, Xin, 0000-0003-3256-2940; Hou, Yong, 0000-0002-0420-0726; Zhu, Shida; Yang, Huanming; Ye, Yunming; Lin, Ge; Chen, Fang; Herrmann, Carl; Eils, Roland, 0000-0002-0034-4036; Shang, Zhouchun, 0000-0002-1740-7961; Xu, Xun Nature Communications 2019
13051 10.1038/s41467-019-09982-5 Cut&Tag For Efficient Epigenomic Profiling Of Small Samples And Single Cells Kaya-Okur, Hatice S.; Wu, Steven J.; Codomo, Christine A.; Pledger, Erica S.; Bryson, Terri D.; Henikoff, Jorja G.; Ahmad, Kami, 0000-0001-8572-6182; Henikoff, Steven Nature Communications 2019
13130 10.1038/s41467-019-11559-1 Mapping Histone Modifications In Low Cell Number And Single Cells Using Antibody-Guided Chromatin Tagmentation (Act-Seq) Carter, Benjamin, 0000-0001-6530-9568; Ku, Wai Lim, 0000-0002-8859-6771; Kang, Jee Youn; Hu, Gangqing; Perrie, Jonathan; Tang, Qingsong; Zhao, Keji, 0000-0001-5559-6233 Nature Communications 2019
13175 10.1038/s41467-019-12630-7 Scale Method For Single-Cell Atac-Seq Analysis Via Latent Feature Extraction Xiong, Lei, 0000-0002-2392-114X; Xu, Kui; Tian, Kang; Shao, Yanqiu; Tang, Lei; Gao, Ge; Zhang, Michael; Jiang, Tao, 0000-0003-3833-4498; Zhang, Qiangfeng Cliff, 0000-0002-4913-0338 Nature Communications 2019
13474 10.1038/s41556-018-0248-3 A Chromatin Integration Labelling Method Enables Epigenomic Profiling With Lower Input Harada, Akihito; Maehara, Kazumitsu; Handa, Tetsuya; Arimura, Yasuhiro; Nogami, Jumpei; Hayashi-Takanaka, Yoko; Shirahige, Katsuhiko; Kurumizaka, Hitoshi; Kimura, Hiroshi, 0000-0003-0854-083X; Ohkawa, Yasuyuki, 0000-0001-6440-9954 Nature Cell Biology 2018
13484 10.1038/s41556-019-0383-5 Profiling Chromatin States Using Single-Cell Itchip-Seq Ai, Shanshan; Xiong, Haiqing; Li, Chen C.; Luo, Yingjie; Shi, Qiang; Liu, Yaxi; Yu, Xianhong; Li, Cheng; He, Aibin, 0000-0002-3489-2305 Nature Cell Biology 2019
14503 10.1038/s41587-019-0113-3 Efficient Integration Of Heterogeneous Single-Cell Transcriptomes Using Scanorama Hie, Brian, 0000-0003-3224-8142; Bryson, Bryan, 0000-0003-1716-6712; Berger, Bonnie, 0000-0002-2724-7228 Nature Biotechnology 2019
14505 10.1038/s41587-019-0147-6 Droplet-Based Combinatorial Indexing For Massive-Scale Single-Cell Chromatin Accessibility Lareau, Caleb A., 0000-0003-4179-4807; Duarte, Fabiana M., 0000-0002-1261-4929; Chew, Jennifer G.; Kartha, Vinay K., 0000-0002-2160-2196; Burkett, Zach D., 0000-0002-5153-485X; Kohlway, Andrew S.; Pokholok, Dmitry; Aryee, Martin J., 0000-0002-6848-1344; Steemers, Frank J.; Lebofsky, Ronald, 0000-0002-3728-6415; Buenrostro, Jason D., 0000-0001-9958-3987 Nature Biotechnology 2019
14508 10.1038/s41587-019-0206-z Massively Parallel Single-Cell Chromatin Landscapes Of Human Immune Cell Development And Intratumoral T Cell Exhaustion Satpathy, Ansuman T., 0000-0002-5167-537X; Granja, Jeffrey M.; Yost, Kathryn E.; Qi, Yanyan; Meschi, Francesca; Mcdermott, Geoffrey P.; Olsen, Brett N.; Mumbach, Maxwell R.; Pierce, Sarah E., 0000-0002-9145-9559; Corces, M. Ryan; Shah, Preyas; Bell, Jason C.; Jhutty, Darisha; Nemec, Corey M.; Wang, Jean; Wang, Li; Yin, Yifeng; Giresi, Paul G.; Chang, Anne Lynn S., 0000-0002-2869-2147; Zheng, Grace X. Y., 0000-0002-5006-3785; Greenleaf, William J., 0000-0003-1409-3095; Chang, Howard Y., 0000-0002-9459-4393 Nature Biotechnology 2019
14520 10.1038/s41587-019-0290-0 High-Throughput Sequencing Of The Transcriptome And Chromatin Accessibility In The Same Cell Chen, Song, 0000-0001-5286-3084; Lake, Blue B., 0000-0002-8637-9044; Zhang, Kun, 0000-0002-7596-5224 Nature Biotechnology 2019
14523 10.1038/s41587-019-0332-7 Single-Cell Multiomic Analysis Identifies Regulatory Programs In Mixed-Phenotype Acute Leukemia Granja, Jeffrey M.; Klemm, Sandy, 0000-0001-7556-6795; Mcginnis, Lisa M.; Kathiria, Arwa S.; Mezger, Anja; Corces, M. Ryan; Parks, Benjamin, 0000-0002-0261-7472; Gars, Eric; Liedtke, Michaela; Zheng, Grace X. Y., 0000-0002-5006-3785; Chang, Howard Y., 0000-0002-9459-4393; Majeti, Ravindra; Greenleaf, William J., 0000-0003-1409-3095 Nature Biotechnology 2019
14578 10.1038/s41588-019-0424-9 High-Throughput Single-Cell Chip-Seq Identifies Heterogeneity Of Chromatin States In Breast Cancer Grosselin, Kevin, 0000-0001-6189-3197; Durand, Adeline, 0000-0002-7423-2504; Marsolier, Justine; Poitou, Adeline; Marangoni, Elisabetta; Nemati, Fariba; Dahmani, Ahmed; Lameiras, Sonia; Reyal, Fabien; Frenoy, Olivia; Pousse, Yannick; Reichen, Marcel; Woolfe, Adam; Brenan, Colin; Griffiths, Andrew D., 0000-0002-0808-3539; Vallot, Celine, 0000-0003-1601-2359; Gerard, Annabelle, 0000-0003-0411-768X Nature Genetics 2019
14761 10.1038/s41592-018-0033-z Saver: Gene Expression Recovery For Single-Cell Rna Sequencing Huang, Mo; Wang, Jingshu; Torre, Eduardo; Dueck, Hannah; Shaffer, Sydney; Bonasio, Roberto; Murray, John I.; Raj, Arjun; Li, Mingyao; Zhang, Nancy R. Nature Methods 2018
14768 10.1038/s41592-018-0229-2 Deep Generative Modeling For Single-Cell Transcriptomics Lopez, Romain; Regier, Jeffrey, 0000-0002-1472-5235; Cole, Michael B.; Jordan, Michael I.; Yosef, Nir, 0000-0001-9004-1225 Nature Methods 2018
14771 10.1038/s41592-018-0254-1 A Test Metric For Assessing Single-Cell Rna-Seq Batch Correction Buttner, Maren, 0000-0002-6189-3792; Miao, Zhichao; Wolf, F. Alexander, 0000-0002-8760-7838; Teichmann, Sarah A., 0000-0002-6294-6366; Theis, Fabian J., 0000-0002-2419-1943 Nature Methods 2018
14776 10.1038/s41592-019-0353-7 Scalable Analysis Of Cell-Type Composition From Single-Cell Transcriptomics Using Deep Recurrent Learning Deng, Yue; Bao, Feng; Dai, Qionghai; Wu, Lani F., 0000-0002-0052-7537; Altschuler, Steven J., 0000-0001-9142-0796 Nature Methods 2019
14777 10.1038/s41592-019-0361-7 Single-Cell Chromatin Immunocleavage Sequencing (Scchic-Seq) To Profile Histone Modification Ku, Wai Lim; Nakamura, Kosuke; Gao, Weiwu; Cui, Kairong; Hu, Gangqing; Tang, Qingsong; Ni, Bing, 0000-0002-4297-5346; Zhao, Keji, 0000-0001-5559-6233 Nature Methods 2019
14778 10.1038/s41592-019-0367-1 Cistopic: Cis-Regulatory Topic Modeling On Single-Cell Atac-Seq Data Bravo Gonzalez-Blas, Carmen, 0000-0003-0973-9410; Minnoye, Liesbeth, 0000-0002-0898-2817; Papasokrati, Dafni, 0000-0002-1524-2155; Aibar, Sara, 0000-0001-6104-7134; Hulselmans, Gert, 0000-0003-2205-1899; Christiaens, Valerie; Davie, Kristofer, 0000-0003-2182-1249; Wouters, Jasper, 0000-0002-7129-2990; Aerts, Stein, 0000-0002-8006-0315 Nature Methods 2019
14787 10.1038/s41592-019-0466-z Joint Analysis Of Heterogeneous Single-Cell Rna-Seq Dataset Collections Barkas, Nikolas, 0000-0002-4675-0718; Petukhov, Viktor; Nikolaeva, Daria; Lozinsky, Yaroslav; Demharter, Samuel; Khodosevich, Konstantin; Kharchenko, Peter V., 0000-0002-6036-5875 Nature Methods 2019
14790 10.1038/s41592-019-0494-8 Scgen Predicts Single-Cell Perturbation Responses Lotfollahi, Mohammad, 0000-0001-6858-7985; Wolf, F. Alexander, 0000-0002-8760-7838; Theis, Fabian J., 0000-0002-2419-1943 Nature Methods 2019
14793 10.1038/s41592-019-0537-1 Data Denoising With Transfer Learning In Single-Cell Transcriptomics Wang, Jingshu; Agarwal, Divyansh, 0000-0003-0404-6877; Huang, Mo, 0000-0002-8399-7525; Hu, Gang; Zhou, Zilu; Ye, Chengzhong; Zhang, Nancy R., 0000-0002-0880-5749 Nature Methods 2019
14797 10.1038/s41592-019-0576-7 Exploring Single-Cell Data With Deep Multitasking Neural Networks Amodio, Matthew; Van Dijk, David; Srinivasan, Krishnan; Chen, William S.; Mohsen, Hussein, 0000-0002-6263-8865; Moon, Kevin R.; Campbell, Allison; Zhao, Yujiao; Wang, Xiaomei; Venkataswamy, Manjunatha; Desai, Anita; Ravi, V.; Kumar, Priti; Montgomery, Ruth, 0000-0002-8661-4454; Wolf, Guy, 0000-0002-6740-059X; Krishnaswamy, Smita, 0000-0001-5823-1985 Nature Methods 2019
14803 10.1038/s41592-019-0619-0 Fast, Sensitive And Accurate Integration Of Single-Cell Data With Harmony Korsunsky, Ilya, 0000-0003-4848-3948; Millard, Nghia; Fan, Jean, 0000-0002-0212-5451; Slowikowski, Kamil; Zhang, Fan, 0000-0002-6102-2970; Wei, Kevin; Baglaenko, Yuriy, 0000-0002-9020-6824; Brenner, Michael; Loh, Po-Ru, 0000-0001-5542-9064; Raychaudhuri, Soumya, 0000-0002-1901-8265 Nature Methods 2019
14807 10.1038/s41592-019-0691-5 Single-Cell Multimodal Omics: The Power Of Many Zhu, Chenxu; Preissl, Sebastian; Ren, Bing Nature Methods 2020
14808 10.1038/s41592-019-0692-4 Computational Methods For Single-Cell Omics Across Modalities Efremova, Mirjana; Teichmann, Sarah A., 0000-0002-6294-6366 Nature Methods 2020
14871 10.1038/s41594-019-0323-x An Ultra High-Throughput Method For Single-Cell Joint Analysis Of Open Chromatin And Transcriptome Zhu, Chenxu, 0000-0003-4216-6562; Yu, Miao; Huang, Hui; Juric, Ivan; Abnousi, Armen, 0000-0003-1822-0928; Hu, Rong; Lucero, Jacinta; Behrens, M. Margarita; Hu, Ming; Ren, Bing, 0000-0002-5435-1127 Nature Structural & Molecular Biology 2019
15050 10.1038/s42256-019-0037-0 Clustering Single-Cell Rna-Seq Data With A Model-Based Deep Learning Approach Tian, Tian, 0000-0001-6147-1082; Wan, Ji; Song, Qi; Wei, Zhi, 0000-0001-6059-4267 Nature Machine Intelligence 2019
16407 10.1073/pnas.1820006116 Scmerge Leverages Factor Analysis, Stable Expression, And Pseudoreplication To Merge Multiple Single-Cell Rna-Seq Datasets Lin, Yingxin; Ghazanfar, Shila; Wang, Kevin Y. X.; Gagnon-Bartsch, Johann A.; Lo, Kitty K.; Su, Xianbin; Han, Ze-Guang; Ormerod, John T.; Speed, Terence P.; Yang, Pengyi, 0000-0003-1098-3138; Yang, Jean Yee Hwa, 0000-0002-5271-2603 Proceedings Of The National Academy Of Sciences 2019
17019 10.1093/bioinformatics/btz625 Bbknn: Fast Batch Alignment Of Single Cell Transcriptomes Pola<U+0144>ski, Krzysztof; Young, Matthew D; Miao, Zhichao; Meyer, Kerstin B; Teichmann, Sarah A; Park, Jong-Eun Bioinformatics 2019
18806 10.1126/science.aau0730 Joint Profiling Of Chromatin Accessibility And Gene Expression In Thousands Of Single Cells Cao, Junyue, 0000-0003-4097-489X; Cusanovich, Darren A., 0000-0001-6889-0095; Ramani, Vijay, 0000-0003-3345-5960; Aghamirzaie, Delasa; Pliner, Hannah A., 0000-0003-1484-6501; Hill, Andrew J.; Daza, Riza M., 0000-0003-1635-8675; Mcfaline-Figueroa, Jose L., 0000-0003-4387-1511; Packer, Jonathan S., 0000-0003-4025-0007; Christiansen, Lena, 0000-0003-1386-4871; Steemers, Frank J.; Adey, Andrew C., 0000-0001-7648-8717; Trapnell, Cole, 0000-0002-8105-4347; Shendure, Jay, 0000-0002-1516-1865 Science 2018
20005 10.1186/s12859-018-2226-y Drimpute: Imputing Dropout Events In Single Cell Rna Sequencing Data Gong, Wuming; Kwak, Il-Youp; Pota, Pruthvi; Koyano-Nakagawa, Naoko; Garry, Daniel J. Bmc Bioinformatics 2018